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Updated: May 14, 2026

Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications
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Published on: April 14, 2015

CUBED: Universal combinatorial barcoding platform for highly multiplexed digital PCR.

Dong Dong Liu1, Cheng Qian2, Wei Ting Loh2

  • 1Department of Biomedical Engineering and Institute for Health Innovation and Technology, National University of Singapore, 119077, Singapore; School of Medicine, Shanghai University, Shanghai, 200444, China.

Biosensors & Bioelectronics
|May 12, 2026
PubMed
Summary
This summary is machine-generated.

A new platform called Combinatorial Universal Barcode End-point Digital PCR (CUBED) allows for highly multiplexed nucleic acid detection. This method enhances accuracy and scalability for applications in diagnostics and research.

Keywords:
DNA barcodeDigital PCRError detectionHigh-throughput screeningMultiplexingSARS-CoV-2

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Multiplexed molecular assays are crucial for diverse applications, including pathogen detection and genetic analysis.
  • Current methods face limitations in multiplexing capacity due to fluorescence channel constraints.

Purpose of the Study:

  • To introduce CUBED (Combinatorial Universal Barcode End-point Digital PCR), a novel platform for high-throughput, multiplexed nucleic acid detection.
  • To demonstrate the platform's ability to overcome fluorescence channel limitations using combinatorial barcoding and multi-amplitude probe labeling.

Main Methods:

  • CUBED utilizes combinatorial color barcoding and multi-amplitude probe labeling for expanded multiplexing.
  • An integrated error-detection scheme ensures robust barcode decoding by minimizing signal dropout.
  • The platform is compatible with standard endpoint digital PCR instruments.

Main Results:

  • Accurate quantitative detection and discrimination of 26 ternary barcodes using three fluorescence channels.
  • Resolution of 20 binary barcodes using a six-channel system.
  • Successful application to pooled SARS-CoV-2 RNA detection across 20 barcoded samples, confirming quantitative accuracy and scalability.

Conclusions:

  • CUBED offers a high-throughput, error-tolerant solution for multiplexed nucleic acid detection.
  • The platform significantly expands multiplexing capacity beyond conventional limits.
  • CUBED is suitable for both research and clinical diagnostic applications.